Förster Resonance Energy Transfer (FRET) combined with single-molecule spectroscopy probes macromolecular structure and dynamics and identifies coexisting conformational states. We review recent methodological developments in integrative structural modeling by satisfying spatial restraints on networks of FRET pairs (hybrid-FRET). We discuss procedures to incorporate prior structural knowledge and to obtain optimal distance networks. Finally, a workflow for hybrid-FRET is presented that automates integrative structural modeling and experiment planning to put hybrid-FRET on rails. To test this workflow, we simulate realistic single-molecule experiments and resolve three protein conformers, exchanging at 30μs and 10ms, with accuracies of 1-3Å RMSD versus the target structure. Incorporation of data from other spectroscopies and imaging is also discussed.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.sbi.2016.11.012 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Steroids and steroid-like compounds alter the ion permeability of phospholipid bilayers distinct interactions with lipids and interfacial water.
Phys Chem Chem Phys
January 2025
School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia QLD 4072, Australia.
Steroids are organic compounds found in all forms of biological life. Besides their structural roles in cell membranes, steroids act as signalling molecules in various physiological processes and are used to treat inflammatory conditions. It has been hypothesised that in addition to their well-characterised genomic and non-genomic pathways, steroids exert their biological or pharmacological activities an indirect, nonreceptor-mediated membrane mechanism caused by steroid-induced changes to the physicochemical properties of cell membranes.
View Article and Find Full Text PDFClimate Change Drives Changes in the Size and Composition of Fungal Communities Along the Soil-Seedling Continuum of Schima superba.
Mol Ecol
January 2025
ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, China.
Plant microbiomes have a major influence on forest structure and functions, as well as tree fitness and evolution. However, a comprehensive understanding of variations in fungi along the soil-plant continuum, particularly within tree seedlings, under global warming is lacking. Here, we investigated the dynamics of fungal communities across different compartments (including bulk soil and rhizosphere soil) and plant organs (including the endosphere of roots, stems and leaves) of Schima superba seedlings exposed to experimental warming and drought using AccuITS absolute quantitative sequencing.
View Article and Find Full Text PDFA computational study of the ternary mixtures of NaPF-EC and choline glycine ionic liquid.
Phys Chem Chem Phys
January 2025
Institute of Science and Technology, Federal University of São Paulo, 12247-014, São José dos Campos, São Paulo, Brazil.
This study investigates the structural and dynamic properties of ternary mixtures composed of NaPF, ethylene carbonate (EC), and the ionic liquid choline glycine (ChGly), with a focus on their potential as electrolytes for supercapacitors. The combination of NaPF-EC, known for its high ionic conductivity, with the biodegradable and environmentally friendly ChGly offers a promising approach to enhancing electrolyte performance. Through molecular simulations, we analyze how the inclusion of small concentrations of ChGly affects key properties such as density, cohesive energy, and ion mobility.
View Article and Find Full Text PDFInhibitory Effect of Human Anti-CA I Autoantibodies and Development of Monoclonal Antibody mAb 2B8 Targeting Carbonic Anhydrase I.
Mediators Inflamm
December 2024
Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia.
Spontaneous tumor regression is a recognized phenomenon across various cancer types. Recent research emphasizes the alterations in autoantibodies against carbonic anhydrase I (CA I) (anti-CA I) levels as potential prognostic markers for various malignancies. Particularly, autoantibodies targeting CA I and II appear to induce cellular damage by inhibiting their respective protein's catalytic functions.
View Article and Find Full Text PDFThe zebrafish is a valuable model organism for studying cardiac development and diseases due to its many shared aspects of genetics and anatomy with humans and ease of experimental manipulations. Computational fluid-structure interaction (FSI) simulations are an efficient and highly controllable means to study the function of cardiac valves in development and diseases. Due to their small scales, little is known about the mechanical properties of zebrafish cardiac valves, limiting existing computational studies of zebrafish valves and their interaction with blood.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!